relecov-tools/.github/workflows/test_sftp_modules.yml at main · BU-ISCIII/relecov-tools · GitHub

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name: test_sftp_modules

on:
  push:
    branches: "**"
  pull_request_target:
    types: [opened, reopened, synchronize]
    branches: "**"

concurrency:
  group: ${{ github.repository }}-test_sftp_modules
  cancel-in-progress: false

jobs:
  security_check:
    runs-on: ubuntu-latest
    steps:
    - name: Get User Permission
      id: checkAccess
      uses: actions-cool/check-user-permission@v2
      with:
        require: write
        username: ${{ github.triggering_actor }}
    - name: Check User Permission
      if: steps.checkAccess.outputs.require-result == 'false'
      run: |
        echo "${{ github.triggering_actor }} does not have permissions on this repo."
        echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}"
        echo "Job originally triggered by ${{ github.actor }}"
        exit 1

  test_download:
    runs-on: ubuntu-latest
    needs: security_check
    if: github.repository_owner == 'BU-ISCIII'
    strategy:
      max-parallel: 1
      matrix:
        download_options: ["download_only", "download_clean", "delete_only"]
        target_folders: ["", "-t COD-test-1"]

    steps:
    - name: Set up Python 3.12
      uses: actions/setup-python@v3
      with:
        python-version: '3.12'

    - name: Checkout code
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0

    - name: Install package and dependencies
      run: |
        pip install -r requirements.txt
        pip install .

    - name: Load profile config (relecov)
      run: |
        relecov-tools add-extra-config \
          --config_file relecov_tools/conf/initial_config-relecov.yaml --force

    - name: Run sftp_handle tests
      run: |
        python3 tests/test_sftp_modules.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }}
      env:
        TEST_USER: ${{ secrets.TEST_USER }}
        TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }}
        TEST_PORT: ${{ secrets.TEST_PORT }}
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/

  test_wrapper:
    runs-on: ubuntu-latest
    needs: test_download
    if: github.repository_owner == 'BU-ISCIII'
    strategy:
      max-parallel: 1
      matrix:
        download_options: ["download_only", "download_clean"]

    steps:
    - name: Set up Python 3.12
      uses: actions/setup-python@v3
      with:
        python-version: '3.12'

    - name: Checkout code
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0

    - name: Install package and dependencies
      run: |
        pip install -r requirements.txt
        pip install .

    - name: Load profile config (relecov)
      run: |
        relecov-tools add-extra-config \
          --config_file relecov_tools/conf/initial_config-relecov.yaml --force

    - name: Run Wrapper tests
      run: |
        python3 tests/test_wrapper_handle.py --download_option ${{ matrix.download_options }}
      env:
        TEST_USER: ${{ secrets.TEST_USER }}
        TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }}
        TEST_PORT: ${{ secrets.TEST_PORT }}
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/


  test_validate_upload:
    runs-on: ubuntu-latest
    needs: test_wrapper
    if: github.repository_owner == 'BU-ISCIII'

    steps:
    - name: Set up Python 3.12
      uses: actions/setup-python@v3
      with:
        python-version: '3.12'

    - name: Checkout code
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0

    - name: Install package and dependencies
      run: |
        pip install -r requirements.txt
        pip install .

    - name: Load profile config (relecov)
      run: |
        relecov-tools add-extra-config \
          --config_file relecov_tools/conf/initial_config-relecov.yaml --force
    - name: Run validate module with upload files (expected default)
      if: github.repository_owner == 'BU-ISCIII'
      run: |
        python3 tests/test_validate.py \
          -j tests/data/map_validate/processed_metadata_lab_test.json \
          -m tests/data/map_validate/metadata_lab_test.xlsx \
          --upload_files \
          -o tests/data/map_validate/ \
          -s relecov_tools/schema/relecov_schema.json \
          -l tests/data/map_validate/previous_processes_log_summary.json
      env:
        TEST_USER: ${{ secrets.TEST_USER }}
        TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }}
        TEST_PORT: ${{ secrets.TEST_PORT }}
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/